This pine grows at low to middle elevations (up to ca. 1,000 m above sea level) in the coastal hills and mountains of the islands of Japan and South Korea, where the climate is warm temperate (with little or no frost) and moist. These regions would have had a predominantly deciduous angiosperm forest cover, with conifers mixed in especially on poor, water-logged soils and on dry slopes and mountain ridges. Pinus thunbergii would have occupied these habitats as well as those in close proximity to the sea coast. Extensive cultivation has removed the natural vegetation in most areas, but as a pioneer species P. thunbergii has been able to hold its own; it has been much planted in afforestation schemes from where it could spread in adjacent uncultivated areas. Its tolerance of salty winds makes it a species that grows well on the sea coasts of Japan, both naturally and when planted; naturally its trunk becomes bent and the crown flattened under severe exposure.

The wood of this pine is similar to that of the Black pine (Pinus nigra) and is used for general construction, poles, railway sleepers, fences, pallets and crates, flooring, fibreboard, and wood pulp. Japanese Black Pine is mostly used as a windbreak tree and to stabilize sand dunes in coastal areas near urbanization. It is also widely planted as an ornamental tree in Japan and Korea (somewhat less commonly in other countries) and some cultivars have been selected especially in Japan to suit traditional Japanese gardening. It is also being used in bonsai growing. In the USA this species was widely planted for afforestation in coastal areas of New England, until susceptibility to pests and diseases put an end to these schemes and forced the species back to arboreta and parks, where solitary trees are usually safe. Minor uses in Korea are of the needles in pastry and in (medicinal) soft drinks.

Logging is a potential threat if done non-sustainably; this was perhaps the case in the past and locally. Urban development, particularly in coastal areas may also have reduced the area of occupancy in the past. Such losses do not appear to have led to an overall decline.